Yea, I did that...
Had a two week budget rental in PDX. During that period, had to fly to Boston, so made a reservation for a short budget rental at the Boston airport, but keeping my PDX rental for my return. When I got to Boston and went to check in (for some odd reason, I didn't use fastbreak), the desk noticed I had an outstanding rental. They said I couldn't have two budget car rentals at the same time. I argued with them, etc., and they relented. So you might want to "clear the waters" in advance...